NAME

UNAFold.pl — fold an RNA or DNA sequence with lots of output

SYNOPSIS

UNAFold.pl [OPTION]... FILE [FILE]

DESCRIPTION

If one FILE is specified, UNAFold.pl folds the (first) sequence in FILE with hybrid-ss-min, and then computes the h-num and ss-count values. If two FILEs are specified, UNAFold.pl hybridized the first sequence in each FILE with hybrid-min. All output files are named with a prefix which consists of the file name(s) with the extension .seq removed. The loop free energy decomposition is written to prefix.det or prefix.det.html. If boxplot_ng is available, the enrgy dot plot is created in Postscript format and, if possible, in PNG, JPEG or GIF format. Likewise, if sir_graph_ng or sir_graph is available, each structure is drawn in Postscript and, if possible, PNG/JPEG/GIF formats. In addition, each structure is available in XRNA ss format, and the complete set of foldings in RNAML format is written to prefix.rnaml. Finally, in HTML mode, prefix.html contains links to all of the output.

OPTIONS

-n, --NA=RNA2|RNA3|RNA|DNA
set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temp=REAL
set folding temperature to REAL °C. Default is 37.
-N, --sodium=REAL
set Sodium ion concentration to REAL molar. Default is 1.
-M, --magnesium=REAL
set Magnesium ion concentration to REAL molar. Default is 0.
-p, --polymer
use salt corrections for polymers instead of oligomers (the default).
-I, --noisolate
prohibit all isolated basepairs. Isolated basepairs are helices of length 1; that is, they do not stack on another basepair on either side. (See also the --prefilter option below.)
-m, --maxbp=NUMBER
bases farther apart than NUMBER cannot form. Default is no limit.
-c, --constraints=FILE
read a list of constraints from FILE. Constraints must be in the form "P i j k" or "F i j k". These are equivalent to specifying "--prohibit=i,j,k" and "--force=i,j,k", respectively. If FILE is not specified, it defaults to prefix.aux.
-C, --circular
treat sequences as circular rather than linear.
--intra
perform hybridization with intramolecular basepairs.
-P, --percent=REAL
set the energy increment to REAL percent. Defauls is 5.
-W, --window=NUMBER
set the window parameter to NUMBER. Default is determined by sequence length.
-X, --max=NUMBER
set the maximum number of foldings to NUMBER. Default is 100.
--ann=none|p-num|ss-count
optionally produce plots annotated with p-num or ss-count values. Default is none.
--mode=auto|bases|lines
produce structures drawn with bases or lines. Default is auto.
--label=NUMBER
label every NUMBERth base.
--rotate=REAL
rotate structures by REAL degrees.
--run-type=text|html
produce output in plain text (the default) or HTML.
--model=EM|PF
perform an energy minimization (the default) or partition function calculation. In partition function mode, stochastic tracebacks replace the mfold sample and a probability dot plot replaces the energy dot plot.
--circular
treat sequence as circular rather than linear.
--intra
hybridize sequences allowing intramolecular basepairs.

OBSCURE OPTIONS

--allpairs
allow basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
--maxloop=NUMBER
set the maximum size of bulge/interior loops to NUMBER. Default is 30.
--maxas=NUMBER
set the maximum asymmetry of bulge/interior loops to NUMBER. Default is 30.
--nodangle
remove single-base stacking from consideration.
--simple
makes the penalty for multibranch loops constant rather than affine.
--prefilter=value1[,value2]
set the prefilter to filter out all basepairs except those in groups of value2 adjacent basepairs of which value1 can form. value2 is the same as value1 if unspecified. Default is 2 of 2. (See also the --noisolate option above.)

ENVIRONMENT

UNAFOLDDAT
an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. UNAFold.pl looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).

REFERENCES

Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.

Other references which may be useful may be found at http://www.unafold.org/Dinamelt/dinamelt-references.php

SEE ALSO

hybrid(1), hybrid-ss(1), hybrid-intra(1), hybrid-min(1), hybrid-ss-min(1), hybrid-intra-min(1), h-num.pl(1), ss-count.pl(1), ct2rnaml(1)

AUTHORS

Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>

COPYRIGHT

Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.

AVAILABILITY

Both commercial and non-commercial use of UNAFold require a license from RPI; see https://ipo.rpi.edu/invention/unafold-version-40.